There's also a chance that it's a new villain created specifically for the fanfic. This villain could have a unique ability or grudge against Naruto and use it to take away his ability to feel.
It could be Orochimaru. He's always been interested in experimenting on strong ninja. Naruto, being the main character, would be an interesting target for Orochimaru to mess with and cause this condition.
It could be a rogue ninja from another village who has a vendetta against Konoha. This ninja might have a special ability to target Naruto specifically and put him in a critical state.
One possible reason could be a powerful jutsu gone wrong. Maybe he was hit by an enemy's attack that was specifically designed to numb his senses. Another reason might be some kind of psychological trauma. For example, if he witnessed something extremely horrible, his mind might have shut down his ability to feel as a form of self - protection.
It could be a new and powerful villain who has emerged. This villain might have a special ability that catches Naruto off - guard during a fight, leading to his injury.
It could be Danzo. He has always been a bit of a shadowy figure with his own motives in the Naruto series. He might see Naruto as a threat to his power and influence within the village and engineer a situation where Naruto is executed.
It could be Orochimaru. He's always been interested in power and experimenting. Maybe he sees Naruto as a perfect guinea pig to test some new jutsu that goes horribly wrong and causes Naruto to explode.
It could be a rogue ninja from another village who has a vendetta against Naruto. This ninja might have set a very elaborate trap that made it seem like Naruto was killed and left his body in a place where his friends would find him and think he was dead.
Maybe he's been cursed by a powerful enemy. In many fanfics, an enemy might use a dark jutsu to take away Naruto's ability to feel. It could be a way to weaken him both physically and mentally.
Maybe some of the more conservative village elders. They have always been a bit wary of Naruto because of the Nine - Tails inside him. So they might be behind his capture in the fanfiction.
It could be Madara Uchiha. He was always seeking power and new ways to achieve his goals. Turning Naruto into a weapon would be a great advantage for him in his plans to reshape the ninja world.
With the new characters introduced in the fanfic, if there are any, Naruto's lack of feeling could create an interesting dynamic. They might either be intrigued and want to help, or they might take advantage of his situation. And for Naruto, he would have to rely on others in a different way than before, which could either strengthen or strain his relationships depending on how others react.